XKCD is my favourite comic. It's very intellemectual. Link
Hipster Hitler is a relatively new one, but still bloody hilarious. Link
I'm a big fan of Xkcd as well. And I just read the first comic on Hipster Hitler, and I'm in love already.
Another one I like to frequent is Awkward Zombie. Link She makes all her comics and whatnot based off of video games. They're pretty good. Just hit the little 'Comics' tab on the left if you want to see some.